Abstract
ABSTRACTThe members of the OM43 clade of Betaproteobacteria are abundant coastal methylotrophs with a range of carbon-utilizing capabilities. However, their underlying transcriptional and metabolic responses to shifting conditions or different carbon substrates remain poorly understood. We examined the transcriptional dynamics of OM43 isolate NB0046 subjected to various inorganic nutrient, vitamin, and carbon substrate regimes over different growth phases to (i) develop a quantitative model of its mRNA content; (ii) identify transcriptional markers of physiological activity, nutritional state, and carbon and energy utilization; and (iii) identify pathways involved in methanol or naturally occurring dissolved organic matter (DOM) metabolism. Quantitative transcriptomics, achieved through addition of internal RNA standards, allowed for analyses on a transcripts-per-cell scale. This streamlined bacterium exhibited substantial shifts in total mRNA content (ranging from 1,800 to 17 transcripts cell−1 in the exponential and deep stationary phases, respectively) and gene-specific transcript abundances (>1,000-fold increases in some cases), depending on the growth phase and nutrient conditions. Carbon metabolism genes exhibited substantial dynamics, including those for ribulose monophosphate, tricarboxylic acid (TCA), and proteorhodopsin, as well as methanol dehydrogenase (xoxF), which, while always the most abundant transcript, increased from 5 to 120 transcripts cell−1 when cultures were nutrient and vitamin amended. In the DOM treatment, upregulation of TCA cycle, methylcitrate cycle, vitamin, and organic phosphorus genes suggested a metabolic route for this complex mixture of carbon substrates. The genome-wide inventory of transcript abundances produced here provides insight into a streamlined marine bacterium’s regulation of carbon metabolism and energy flow, providing benchmarks for evaluating the activity of OM43 populations in situ.
Highlights
Microbial activities are major drivers of nutrient cycles and energy transfer in marine ecosystems, and the ability to monitor these activities in situ has been enhanced by recently developed genome-enabled technologies
Evidence of a further expanded metabolic range in OM43 clade methylotrophs was recently demonstrated for multiple OM43 strains that were isolated via growth on naturally derived HMW dissolved organic matter (DOM) [19]
OM43 strain NB0046 was originally isolated off the coast of Massachusetts in the United States via dilution to extinction in a seawater medium enriched with naturally occurring HMW DOM [19]
Summary
Microbial activities are major drivers of nutrient cycles and energy transfer in marine ecosystems, and the ability to monitor these activities in situ has been enhanced by recently developed genome-enabled technologies. The genes enabling this expanded metabolic range, as well as their regulation under different environmental conditions, remain unknown Complementing these laboratory observations, environmental surveys are revealing that members of the OM43 clade are active, dynamic members of coastal communities. OM43 xoxF-type methanol dehydrogenase transcripts had higher seasonal abundances in the fall and winter but minimal day-night differences, while in contrast, transcripts for ribosomal proteins and elongation factors displayed some of the largest daynight differences observed in the entire microbial community [22] These results suggest that OM43 members may tightly tune their transcriptome to the environmental conditions of coastal ecosystems, including temporal shifts in nutrient availability and primary production. It is not known which environmental factors are responsible for driving OM43 transcription dynamics
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